PDB-3s0a: Apis mellifera OBP14, native apo-protein

ID or keywords:

Entry

Database: PDB / ID: 3s0a

Title

Apis mellifera OBP14, native apo-protein

Components

OBP14

Keywords

TRANSPORT PROTEIN / all helical protein / unknown odorant molecules / antennae

Function / homology

Function and homology information

odorant binding / extracellular region
Similarity search - Function

Biological species

Apis mellifera (honey bee)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.15 Å

Authors

Spinelli, S. / Lagarde, A. / Iovinella, I. / Tegoni, M. / Pelosi, P. / Cambillau, C.

Citation

Journal: Insect Biochem.Mol.Biol. / Year: 2012
Title: Crystal structure of Apis mellifera OBP14, a C-minus odorant-binding protein, and its complexes with odorant molecules.
Authors: Spinelli, S. / Lagarde, A. / Iovinella, I. / Legrand, P. / Tegoni, M. / Pelosi, P. / Cambillau, C.

History

Deposition	May 13, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 30, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jan 11, 2012	Group: Database references
Revision 1.2	Sep 13, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3s0a.cif.gz	69.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3s0a.ent.gz	52.2 KB	Display	PDB format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s0/3s0a ftp://data.pdbj.org/pub/pdb/validation_reports/s0/3s0a	HTTPS FTP

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Related structure data

Related structure data	3rzsSC 3s0bC 3s0dC 3s0eC 3s0fC 3s0gC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3rzs-d 3s0d-d 3s0f-1 3s0g-1 3zrg-d 3fr2-d 1lic-d 3s0g-2 5ol5-1 3s0f-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: OBP14

13.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	32.410, 37.990, 86.380
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	OBP14 / odorant binding protein 14 Mass: 13553.611 Da / Num. of mol.: 1 / Fragment: UNP residues 18-135 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Apis mellifera (honey bee) / Gene: NP_001035313 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q1W640
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 1.96 Å³/Da / Density % sol: 37.3 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.8 Details: 1.8-1.9 M tri-sodium citrate, 25 mM CHES, pH 9.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.8265
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 8, 2011 / Details: mirrors
Radiation	Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8265 Å / Relative weight: 1
Reflection	Resolution: 1.15→45.1 Å / Num. all: 37980 / Num. obs: 37980 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / B_iso Wilson estimate: 10.2 Å² / R_merge(I) obs: 0.045 / Net I/σ(I): 18.7
Reflection shell	Resolution: 1.15→1.18 Å / Redundancy: 3.1 % / R_merge(I) obs: 0.5 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2422 / % possible all: 86.1

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
MOLREP		phasing
REFMAC	5.5.0109	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RZS

3rzs

Resolution: 1.15→43.19 Å / Cor.coef. F_o:F_c: 0.972 / Cor.coef. F_o:F_c free: 0.957 / SU B: 1.142 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.039 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.17797	1900	5 %	RANDOM
R_work	0.15484	-	-	-
all	0.15602	36080	-	-
obs	0.15602	36080	98.01 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 8.414 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.27 Å²	-0 Å²	0 Å²
2-	-	-0.62 Å²	-0 Å²
3-	-	-	0.35 Å²

Refine analyze

Luzzati coordinate error free: 0.038 Å

Refinement step

Cycle: LAST / Resolution: 1.15→43.19 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	943	0	0	174	1117

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	1025
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	700
X-RAY DIFFRACTION	r_angle_refined_deg	1.481	1.99	1398
X-RAY DIFFRACTION	r_angle_other_deg	0.939	3	1772
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.165	5	142
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.52	27.907	43
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.282	15	228
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.59	15	1
X-RAY DIFFRACTION	r_chiral_restr	0.091	0.2	172
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	1114
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	159
X-RAY DIFFRACTION	r_mcbond_it	1.196	1.5	633
X-RAY DIFFRACTION	r_mcbond_other	0.385	1.5	251
X-RAY DIFFRACTION	r_mcangle_it	1.938	2	1053
X-RAY DIFFRACTION	r_scbond_it	3.043	3	392
X-RAY DIFFRACTION	r_scangle_it	4.68	4.5	332
X-RAY DIFFRACTION	r_rigid_bond_restr	1.132	3	1725

LS refinement shell

Resolution: 1.15→1.18 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.312	128	-
R_work	0.278	2290	-
obs	-	2290	86.17 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	-0.347	0.6833	0.8573	2.2944	0.9768	2.7862	0.0657	0.0239	0.0535	0.2585	-0.0641	0.0081	0.2291	-0.0502	-0.0016	0.0774	0.0003	0.0154	0.0085	-0.0037	0.01	16.076	3.6486	29.3747
2	-0.002	-0.3908	-0.0735	2.777	-0.629	0.3918	-0.009	0.0082	0.0355	0.0166	0.0151	-0.06	0.0316	0.0454	-0.0061	0.0295	-0.0023	0.0031	0.0265	0.0066	0.0278	18.2693	16.6159	24.632
3	0.1607	0.642	0.1966	1.7587	-0.1157	2.4276	0.031	0.0043	-0.0158	0.0705	-0.0402	-0.1415	-0.0695	0.0876	0.0092	0.0192	0.0011	-0.0118	0.0266	0.0038	0.0364	19.1875	25.1344	31.7697
4	0.8408	-0.1701	0.986	0.3201	-1.0043	1.0361	-0.0156	-0.1472	0.1476	0.1215	0.0034	0.0491	-0.0796	0.005	0.0122	0.0566	0.0042	-0.0028	0.0219	-0.0142	0.0579	11.5744	24.2945	36.1154
5	1.406	-0.0935	0.3538	0.9172	0.7148	0.4988	-0.061	0.0391	0.0712	-0.0144	0.0547	0.0488	-0.0087	0.0235	0.0063	0.0214	-0.0092	-0.0081	0.0225	0.0264	0.0454	10.6784	24.3429	26.3656
6	2.1937	0.1999	0.9796	-0.3164	-0.4571	1.9743	0.0067	0.029	-0.1629	-0.0674	0.0189	0.0262	0.1007	-0.0519	-0.0256	0.0255	-0.0127	-0.0303	0.0038	0.0051	0.0749	4.3997	15.0005	21.3281
7	2.3598	0.8691	3.6595	3.4179	-2.2502	4.194	0.2216	-0.3623	0.08	-0.1807	0.1599	0.2098	0.4486	-0.5681	-0.3814	0.0405	-0.0413	-0.0079	0.0775	0.0255	0.0146	-1.1393	11.0066	27.068
8	4.6201	0.5827	-1.6413	0.5004	0.0233	1.878	-0.1759	-0.0839	-0.0687	-0.0684	0.1459	-0.1023	0.1498	-0.0629	0.03	0.0494	-0.0233	0.0192	0.048	-0.0133	0.0126	3.8845	3.0878	37.3525
9	-0.5537	-0.4567	0.5005	3.9922	-2.1334	2.032	-0.0001	-0.0392	0.0671	-0.0821	0.0504	0.0872	0.0884	-0.1081	-0.0503	0.0185	-0.0031	0.002	0.0437	0.0235	0.037	-3.547	10.9796	37.3931
10	1.0873	0.5537	-0.558	0.4444	-0.4601	1.7911	0.0321	0.0006	0.0563	-0.0929	0.0559	0.1479	0.0184	-0.1324	-0.088	0.021	0.0085	-0.0174	0.04	0.0516	0.0852	-1.1501	25.5966	29.0126
11	-0.3429	0.0243	0.0968	2.0393	-1.0686	3.2317	0.0262	-0.0174	0.0632	0.0668	-0.036	0.0813	0.0515	-0.063	0.0098	0.018	-0.0049	0.0152	0.031	0.0217	0.0409	4.471	19.2953	36.9108
12	0.5462	-0.2646	0.6123	0.6778	-0.2323	0.3442	0.0337	0.0096	-0.019	-0.009	-0.0139	0.004	0.0844	0.0278	-0.0198	0.065	0.0142	-0.0093	0.0308	0.0139	0.0051	14.3636	10.0182	38.8647

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 10
2	X-RAY DIFFRACTION	2	A	11 - 20
3	X-RAY DIFFRACTION	3	A	21 - 30
4	X-RAY DIFFRACTION	4	A	31 - 40
5	X-RAY DIFFRACTION	5	A	41 - 50
6	X-RAY DIFFRACTION	6	A	51 - 60
7	X-RAY DIFFRACTION	7	A	61 - 70
8	X-RAY DIFFRACTION	8	A	71 - 80
9	X-RAY DIFFRACTION	9	A	81 - 90
10	X-RAY DIFFRACTION	10	A	91 - 100
11	X-RAY DIFFRACTION	11	A	101 - 109
12	X-RAY DIFFRACTION	12	A	110 - 119

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